A chemical reaction is what makes them light up. The creature or plant or fungus has special cells in which two or more chemicals combine to produce light. It could be within the skin, or it could be deeper inside the fish or creature, but the outer layers would be transparent and clear, so the light would come through. You can get the basics about bioluminescence at wikipedia. Follow the links at the bottom of that page for many more websites about bioluminescence.
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